Just a couple of thoughts on this one. While Pullman is avowedly Atheist, and the novels reflect that, they are not anti-Catholic. They are anti-religion. The Magisterium, while superficially Catholic, is used as a symbol for religion as a whole; the similarities lie in the fact that Catholicism is and was a large, powerful and repressive structure, and naturally any kind of similar structure will resemble it. Had Protestantism been the driving force in Western religion for as long as Catholicism, no doubt the Golden Compass would be attracting more fire from Baptists; had it been Mormonism, Mitt Romney would be speaking out against it during Presidential debates.

In short, while the Magisterium is a symbol for religion as a whole, it is not the symbol for any one religion. That it happens to resemble Catholicism, this is more a matter of cultural imprinting than anything else.